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The Whole Genome Sequencing Coverage Plot

Introduction

The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth information, variants and DNA Gene features

Dependencies

Software Version

Programming Languages

Tools/libraries

Installation

Install by pip

pip install wgscovplot

Install by conda

conda install -c bioconda wgscovplot

If the installation was successful, you should be able to type wgscovplot --help and get a help message on how to use the tool.

Usage

Usage: wgscovplot [OPTIONS]

Options:
 -s, --samples-data PATH         List of Sample Names, Coverage, VCF File
                                 [required]
 -o, --output-html PATH          Output Interactive HTML Coverage Plot
                                 [default: coverage_plot.html]
 -r, --ref-seq PATH              Reference genome sequences file  [required]
 -b, --bed PATH                  Bed file
 -g, --genbank PATH              Genbank file contains features of reference
                                 sequence  [required]
 --verbose / --no-verbose        Verbose logs  [default: no-verbose]
 --version / --no-version        Print wgscovplot version and exit
 --install-completion [bash|zsh|fish|powershell|pwsh]
                                 Install completion for the specified shell.
 --show-completion [bash|zsh|fish|powershell|pwsh]
                                 Show completion for the specified shell, to
                                 copy it or customize the installation.
 --help                          Show this message and exit.

Prepare Samples Data

The tool currently requires users to prepare samples data file (tsv file) is as the format below. We are updating the tool so that user just simply provide directory and file's identifiers

Sample Name Depth file Variant vcf
Sample-01 path/to/sample-01-coverage-depth path/to/sample-01-variant-vcf
Sample-02 path/to/sample-02-coverage-depth path/to/sample-02-variant-vcf
Sample-03 path/to/sample-03-coverage-depth path/to/sample-03-variant-vcf

Note that no header is needed

Other data:

Output:

The tool will generate the Coverage Plot for samples in HTML file

Command

wgscovplot -s samples.tsv -r reference.fasta -o sequencing_coverage_plot.html -g sequence_genbank.gb

Authors

License

Copyright 2021 Canadian Food Inspection Agency of Canada, Government of Canada.

Distributed under the MIT license.

What happens when the number of samples shown on the chart changed?

What happens when browser zoom is set more than 100%?

How many simultaneous samples are on the chart for the best view?

What will you do when the plot is distorted or minimized?

Sample Name Mean Coverage Median Coverage Genome Coverage(>= 10x) Low Coverage Positions (< 10X) No Coverage Positions (0X) Low Coverage Regions (< 10X) No Coverage Regions (0X)
CFIA-Sample-01 4924.1X 4668.0X 99.62% 114 93 1-10; 29800-29903 1-2; 29813-29903
CFIA-Sample-02 10426.6X 8680.0X 99.62% 115 104 1-5; 7-7; 29795-29903 29800-29903
CFIA-Sample-03 7669.0X 6955.0X 99.63% 110 100 1-2; 29796-29903 29804-29903
CFIA-Sample-04 7303.1X 3078.0X 99.57% 128 117 1-19; 29795-29903 1-16; 29803-29903
CFIA-Sample-05 8065.9X 5425.0X 99.08% 276 103 1-23; 9416-9416; 9423-9423; 9427-9427; 9431-9432; 9454-9454; 9467-9468; 9470-9472; 9475-9477; 9492-9493; 9501-9503; 9511-9511; 9526-9526; 9537-9542; 9547-9547; 9555-9555; 9566-9566; 9569-9569; 9588-9588; 9597-9598; 9618-9619; 9621-9621; 9624-9627; 9671-9671; 9676-9676; 9680-9681; 9700-9701; 9711-9711; 9715-9716; 9734-9734; 9740-9741; 9756-9757; 9762-9762; 9767-9770; 9773-9773; 9777-9781; 9794-9794; 9799-9800; 9812-9812; 9820-9820; 9824-9824; 9828-9828; 9842-9843; 9858-9860; 9867-9867; 9870-9871; 9887-9887; 9891-9894; 9913-9913; 9918-9918; 9923-9923; 9928-9928; 9932-9933; 9937-9937; 9944-9945; 9965-9965; 9988-9988; 9995-9995; 10010-10010; 10023-10024; 10029-10029; 10041-10041; 10060-10060; 10066-10066; 10075-10077; 10081-10081; 10088-10090; 10095-10095; 10110-10110; 10119-10121; 10133-10134; 10138-10139; 10170-10171; 10179-10179; 10185-10186; 10190-10190; 10192-10193; 10195-10197; 10202-10204; 10207-10207; 10213-10213; 10261-10262; 10265-10265; 10296-10296; 10299-10300; 10310-10310; 29795-29903 1-1; 29802-29903
CFIA-Sample-06 7371.8X 4883.0X 95.90% 1225 108 1-20; 9402-10325; 19699-19699; 19701-19703; 19709-19709; 19712-19712; 19715-19725; 19728-19729; 19736-19738; 19749-19755; 19764-19764; 19770-19770; 19774-19774; 19777-19779; 19782-19809; 19813-19816; 19818-19820; 19828-19828; 19837-19837; 19843-19849; 19855-19865; 19868-19868; 19877-19888; 19891-19891; 19894-19894; 19897-19897; 19900-19901; 19907-19919; 19931-19934; 19939-19944; 19950-19951; 19962-19962; 19965-19967; 19970-19975; 19978-19986; 19999-20000; 20002-20003; 20009-20012; 20017-20017; 20023-20024; 20032-20033; 20110-20112; 20114-20116; 20191-20191; 20208-20208; 29796-29903 1-10; 29806-29903
CFIA-Sample-07 7303.1X 3078.0X 99.57% 128 117 1-19; 29795-29903 1-16; 29803-29903
CFIA-Sample-08 8065.9X 5425.0X 99.08% 276 103 1-23; 9416-9416; 9423-9423; 9427-9427; 9431-9432; 9454-9454; 9467-9468; 9470-9472; 9475-9477; 9492-9493; 9501-9503; 9511-9511; 9526-9526; 9537-9542; 9547-9547; 9555-9555; 9566-9566; 9569-9569; 9588-9588; 9597-9598; 9618-9619; 9621-9621; 9624-9627; 9671-9671; 9676-9676; 9680-9681; 9700-9701; 9711-9711; 9715-9716; 9734-9734; 9740-9741; 9756-9757; 9762-9762; 9767-9770; 9773-9773; 9777-9781; 9794-9794; 9799-9800; 9812-9812; 9820-9820; 9824-9824; 9828-9828; 9842-9843; 9858-9860; 9867-9867; 9870-9871; 9887-9887; 9891-9894; 9913-9913; 9918-9918; 9923-9923; 9928-9928; 9932-9933; 9937-9937; 9944-9945; 9965-9965; 9988-9988; 9995-9995; 10010-10010; 10023-10024; 10029-10029; 10041-10041; 10060-10060; 10066-10066; 10075-10077; 10081-10081; 10088-10090; 10095-10095; 10110-10110; 10119-10121; 10133-10134; 10138-10139; 10170-10171; 10179-10179; 10185-10186; 10190-10190; 10192-10193; 10195-10197; 10202-10204; 10207-10207; 10213-10213; 10261-10262; 10265-10265; 10296-10296; 10299-10300; 10310-10310; 29795-29903 1-1; 29802-29903